Project: Computational Methods to Study Gene Transcription Initiation Patterns

Software & Tools

1. FlexSLiM is a software tool for reliable discovery of short linear motifs in protein sequences. By testing on simulated data and benchmark experimental data, we demonstrated that FlexSLiM more effectively identifies short linear motifs than existing methods. We here provide FlexSLim as a general tool that will advance the understanding of short linear motifs, which will facilitate the research on protein targeting signals, protein post-translational modifications, and many others.

Code Download Here.

2. D-mirT is a software tool based on two-stream deep learning model to identify condition-specific miRNA TSSs. It is a natural fit for the integration of low-resolution transcription activity marker such as DNase and H3K4me3 data and high-resolution sequence data. D-miRT model is trained by integrating genome-scale CAGE experiments from FANTOM project and epigenomic marker data from ENCODE project over five common cell lines.